<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Sat, Jun 28, 2014 at 8:00 AM, Mark Adams <span dir="ltr"><<a href="mailto:mfadams@lbl.gov" target="_blank">mfadams@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">And this is the configure log.</div></blockquote><div><br></div><div>Here is the problem:</div><div><br></div><div><div>Executing: mpixlcxx_r -c -o /tmp/petsc-ByVZS6/PETSc.utilities.missing/conftest.o -I/tmp/petsc-ByVZS6/config.compilers -I/tmp/petsc-ByVZS6/config.setCompilers -I/tmp/petsc-ByVZS6/config.functions -I/tmp/petsc-ByVZS6/config.types -I/tmp/petsc-ByVZS6/PETSc.utilities.missing -O5 -qhot=level=0 -qsimd=auto -qmaxmem=-1 -qstrict -qstrict_induction -+ /tmp/petsc-ByVZS6/PETSc.utilities.missing/conftest.cc </div>
<div>Possible ERROR while running compiler: exit code 256</div><div>stderr:</div><div>"/tmp/petsc-ByVZS6/PETSc.utilities.missing/conftest.cc", line 4.9: 1540-0848 (S) The macro name "_GNU_SOURCE" is already defined with a different definition.</div>
<div>Source:</div><div>#include "confdefs.h"</div><div>#include "conffix.h"</div><div>#define _BSD_SOURCE</div><div>#define _GNU_SOURCE</div><div><br></div><div>#ifdef PETSC_HAVE_UNISTD_H</div><div>#include <unistd.h></div>
<div>#endif</div><div>#ifdef PETSC_HAVE_NETDB_H</div><div>#include <netdb.h></div><div>#endif</div><div><br></div><div>int main() {</div><div><br></div><div>int (*getdomainname_ptr)(char*,size_t) = getdomainname;</div>
<div>char test[10];</div><div>if (getdomainname_ptr(test,10)) return 1;</div><div>;</div><div> return 0;</div><div>}</div><div> Compile failed inside link</div></div><div><br></div><div>Jed, what is going on with the _GNU_SOURCE crap?</div>
<div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">
<span class=""><font color="#888888"><div>Mark</div><div><br></div></font></span></div><div class=""><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">On Sat, Jun 28, 2014 at 4:48 PM, Mark Adams <span dir="ltr"><<a href="mailto:mfadams@lbl.gov" target="_blank">mfadams@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra">PETSc,</div><div class="gmail_extra">
<br></div><div class="gmail_extra">I am trying to build a code with PETSc on Mira and I seem to be getting some conflicting declarations.</div>
<div class="gmail_extra">
I have pulled from dev and reconfigured PETSc today. Any ideas?</div><div class="gmail_extra"><br></div><div class="gmail_extra">Mark</div><div class="gmail_extra"><br></div><div class="gmail_extra"><div class="gmail_extra">
mpixlcxx_r -g -DCH_SPACEDIM=3 -DCH_Linux -DCH_MPI -DMPICH_SKIP_MPICXX -ULAM_WANT_MPI2CPP -DMPI_NO_CPPBIND -DCH_USE_SETVAL -DCH_USE_COMPLEX -DCH_USE_MEMORY_TRACKING -DCH_USE_64 -DCH_USE_DOUBLE -DCH_USE_HDF5 -I/soft/libraries/hdf5/1.8.10/cnk-xl/current/include -DH5_USE_16_API -DCH_USE_PETSC -I/home/adams/petsc_public/include -I/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include -I/gpfs/mira-home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include -I/bgsys/drivers/V1R2M1/ppc64/comm/include -I/bgsys/drivers/V1R2M1/ppc64/comm/lib/xl -I/bgsys/drivers/V1R2M1/ppc64 -I/bgsys/drivers/V1R2M1/ppc64/comm/sys/include -I/bgsys/drivers/V1R2M1/ppc64/spi/include -I/bgsys/drivers/V1R2M1/ppc64/spi/include/kernel/cnk -DCH_FORT_UNDERSCORE -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/AMRTools -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools -I/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BaseTools -DCH_LANG_CC -c PetscCompGrid.cpp -o o/3d.Linux.64.mpixlcxx_r.mpixlf77_r.DEBUG.MPI.PETSC/PetscCompGrid.o</div>
<div class="gmail_extra">"/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", line 447.14: 1540-1091 (W) The friend declaration "bdryLo" specifies a default argument expression and is not a definition.</div>
<div class="gmail_extra">"/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", line 460.14: 1540-1091 (W) The friend declaration "bdryHi" specifies a default argument expression and is not a definition.</div>
<div class="gmail_extra">"/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", line 490.14: 1540-1091 (W) The friend declaration "adjCellLo" specifies a default argument expression and is not a definition.</div>
<div class="gmail_extra">"/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/ProblemDomain.H", line 521.14: 1540-1091 (W) The friend declaration "adjCellHi" specifies a default argument expression and is not a definition.</div>
<div class="gmail_extra">"/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", line 7.5: 1540-0400 (S) "getdomainname(char *, size_t)" has a conflicting declaration.</div><div class="gmail_extra">
"/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/unistd.h", line 916.12: 1540-0424 (I) "getdomainname" is declared on line 916 of "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/unistd.h".</div>
<div class="gmail_extra">"/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", line 8.8: 1540-0400 (S) "drand48()" has a conflicting declaration.</div><div class="gmail_extra">"/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h", line 395.15: 1540-0424 (I) "drand48" is declared on line 395 of "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h".</div>
<div class="gmail_extra">"/home/adams/petsc_public/arch-bgq-ibm-opt-64idx/include/petscfix.h", line 9.8: 1540-0400 (S) "srand48(long)" has a conflicting declaration.</div><div class="gmail_extra">"/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h", line 409.13: 1540-0424 (I) "srand48" is declared on line 409 of "/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/sys-include/stdlib.h".</div>
<div class="gmail_extra">"/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/IntVectSet.H", line 387.3: 1540-1091 (W) The friend declaration "refine" specifies a default argument expression and is not a definition.</div>
<div class="gmail_extra">"/gpfs/mira-home/adams/Chombo/lib/src/AMRElliptic/../../src/BoxTools/IntVectSet.H", line 409.3: 1540-1091 (W) The friend declaration "coarsen" specifies a default argument expression and is not a definition.</div>
<div class="gmail_extra">gmake[2]: *** [o/3d.Linux.64.mpixlcxx_r.mpixlf77_r.DEBUG.MPI.PETSC/PetscCompGrid.o] Error 1</div><div class="gmail_extra">gmake[1]: *** [AMRElliptic] Error 2</div><div class="gmail_extra">make: *** [AMRElliptic] Error 2</div>
<div class="gmail_extra">[adams@miralac1 execBCG]$ </div></div></div>
</blockquote></div><br></div>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener
</div></div>